Biomedical subjects

R Ghirlando

Publications and source records attributed to R Ghirlando.

36 records · Page 2Linked to original sources

PubMed1997

Nucleosomes: a solution to a crowded intracellular environment?

The emergence of eukaryotes was accompanied by two major events that concern their genome and are of crucial significance when considered in terms of macromolecular crowding: (i) a substantial increase in the amount of DNA, and (ii) its confinement within a defined space. The resulting highly crowded environment would have strongly promoted DNA self-assembly processes, leading to extremely condensed and thermodynamically stable DNA aggregates. Such structural transitions have indeed been observed in vitro, as well as in virtually all cellular systems in which a nucleosomal assembly is absent. In this appear we raise the hypothesis that upon transition from prokaryotic systems to eukaryotes, the nucleosomes were rendered essential in order to negate extensive DNA condensation processes that would have resulted from excluded volume effects. By suppressing such processes, the nucleosomes act to maintain and regulate the conformational space of the DNA, thus enabling conformational flexibility and reversible structural modulations.

Animals↗

PubMed1997

Interaction of the low-affinity receptor CD23/Fc epsilonRII lectin domain with the Fc epsilon3-4 fragment of human immunoglobulin E.

CD23/Fc epsilonRII, the low-affinity receptor for IgE, is a multifunctional protein of importance in blood cell development and the immune system. We have studied the interaction of CD23 with IgE in solution using hydrodynamic methods applied to recombinant fragments of both ligands: sCD23, corresponding to the soluble lectin domain of CD23, and Fc epsilon3-4, a dimer of the C epsilon3-C epsilon4 sequence of IgE. The hydrodynamic, spectroscopic, and biological properties of these fragments suggest that they have a fully native structure. Sedimentation equilibrium studies on mixtures of sCD23 and Fc epsilon3-4 indicate that IgE has two binding sites for CD23, each characterized by affinities of approximately 10(5) M(-1). Analysis of the sedimentation as a function of temperature allows conclusions to be drawn about the thermodynamics of binding at the two sites. Binding at the first site is characterized by large changes in enthalpy (delta H(degree)To = -2.1 +/- 3.3 kcal mol(-1)) and heat capacity (delta Cp(degree) = -320 +/- 320 cal mol(-1) K(-1)), whereas binding at the second site is characterized by small changes in enthalpy (delta H(degree)To = 0.1 +/- 5.6 kcal mol(-1)) and heat capacity (delta Cp(degree) = -140 +/- 550 cal mol(-1) K(-1)). In native CD23, there are two or three lectin domains, associated through an alpha-helical coiled-coil stalk. The predicted structure of the CD23 oligomers and symmetry considerations rule out the possibility of two lectin domains from one oligomer binding to identical sites in IgE. The notion of two types of interaction in the 2:1 complex between CD23 and IgE is consistent with the thermodynamic data presented.

Binding Sites↗

PubMed1997

Basis of the 1:1 stoichiometry of the high affinity receptor Fc epsilon RI-IgE complex.

A soluble fragment of the high-affinity IgE receptor Fc epsilon RI alpha-chain (sFc epsilon RI alpha) binds to the Fc fragment of IgE (IgE-Fc) as a 1:1 complex. IgE-Fc consists of a dimer of the C epsilon 2, C epsilon 3 and C epsilon 4 domains of the epsilon-heavy chain of IgE. This region of IgE has been modelled on the crystal structure of the Fc region of IgG1, which exhibits twofold rotational symmetry. This implies that IgE should be divalent with respect to its ligands. X-ray scattering studies reveal however that the twofold rotational symmetry of IgE-Fc is perturbed by a bend in the linker region between the C epsilon 2 and C epsilon 3 domains. The 1:1 stoichiometry could then arise from the conformational asymmetry or from steric occlusion of one of the sites by the overhanging C epsilon 2 domains. To test this hypothesis we have expressed a recombinant epsilon-chain fragment containing C epsilon 3 and C epsilon 4. This product, Fc epsilon 3-4, is secreted from cells as a disulphide linked dimer and binds with higher affinity than either IgE or IgE-Fc to cell surface Fc epsilon RI. Titration experiments, together with molecular mass measurements of the Fc epsilon 3-4/sFc epsilon RI alpha complex, reveal that Fc epsilon 3-4 binds only a single receptor molecule. This excludes the possibility that steric hindrance by C epsilon 2 accounts for the unexpected stoichiometry.

Binding Sites↗

PubMed1996

The single Cys2-His2 zinc finger domain of the GAGA protein flanked by basic residues is sufficient for high-affinity specific DNA binding.

Specific DNA binding to the core consensus site GAGAGAG has been shown with an 82-residue peptide (residues 310-391) taken from the Drosophila transcription factor GAGA. Using a series of deletion mutants, it was demonstrated that the minimal domain required for specific binding (residues 310-372) includes a single zinc finger of the Cys2-His2 family and a stretch of basic amino acids located on the N-terminal end of the zinc finger. In gel retardation assays, the specific binding seen with either the peptide or the whole protein is zinc dependent and corresponds to a dissociation constant of approximately 5 x 10(-9) M for the purified peptide. It has previously been thought that a single zinc finger of the Cys2-His2 family is incapable of specific, high-affinity binding to DNA. The combination of an N-terminal basic region with a single Cys2-His2 zinc finger in the GAGA protein can thus be viewed as a novel DNA binding domain. This raises the possibility that other proteins carrying only one Cys2-His2 finger are also capable of high-affinity specific binding to DNA.

Amino Acid Sequence↗

PubMed1996

A soluble active mutant of HIV-1 integrase: involvement of both the core and carboxyl-terminal domains in multimerization.

Structural studies of human immunodeficiency virus type 1 (HIV-1) integrase have been impeded by the low solubility of the protein. By systematic replacement of hydrophobic residues, we previously identified a single amino acid change (F185K) that dramatically improved the solubility of the catalytic domain of HIV-1 integrase and enabled the structure to be determined by x-ray crystallography. We have introduced the same mutation into full-length HIV-1 integrase. The resulting recombinant protein is soluble and fully active in vitro, whereas, HIV-1 carrying the mutation is replication-defective due to improper virus assembly. Analysis of the recombinant protein by gel filtration and sedimentation equilibrium demonstrate a dimer-tetramer self-association. We find that the regions involved in multimerization map to both the catalytic core and carboxyl-terminal domains. The dramatically improved solubility of this protein make it a good candidate for structural studies.

Amino Acid Sequence↗

PubMed1996

Dissociation kinetics of RepA dimers: implications for mechanisms of activation of DNA binding by chaperones.

BACKGROUND: The replication initiator of plasmid P1, RepA, binds DNA as monomer. The binding is stimulated by the chaperones DnaJ, DnaK and GrpE of Escherichia coli. Two models of chaperone action have been proposed. (i) Chaperones dissociate RepA dimers, which are inactive in DNA binding, into active monomers. (ii) The dissociation occurs spontaneously but the monomeric products require the chaperones for refolding into the active form. The latter model was based on the observation that RepA diluted 1000-fold below the K(D) for dimer dissociation, still required the chaperones for DNA binding. RESULTS: We have confirmed that under the condition of DNA binding experiments, the RepA dimers dissociate reversibly into monomers with a K(D) value of 1.1 +/- 0.1 microM. In the vicinity of this concentration, the sedimentation coefficient of RepA was concentration dependent, allowing estimation of s(20,w) coefficients for the RepA monomer (2.95 S) and dimer (4.01 S). Dynamic light scattering experiments indicated an increase of the monomer fraction within 5 min of RepA dilution. Circular dichroism (CD) measurements were consistent with these results. CONCLUSION: RepA monomerization is efficient without the mediation of chaperones. They are required to activate RepA most likely because they are needed to re-fold RepA monomers.

Circular Dichroism↗

PubMed1995

Stoichiometry and thermodynamics of the interaction between the Fc fragment of human IgG1 and its low-affinity receptor Fc gamma RIII.

IgG-Fc receptors, cell surface glycoproteins binding the Fc region of antibodies, play a crucial role in the immune system. To better understand the nature of the recognition process, we have examined the interaction between huIgG1-Fc and a soluble fragment of huFc gamma RIII (sCD16). Analytical ultracentrifugation experiments clearly demonstrate that IgG1-Fc and sCD16 interact weakly to form a 1:1 complex with an association constant of 1.7 x 10(5) M-1 in PBS at 22.0 degrees C. The thermodynamic parameters, obtained from the temperature dependence of the equilibrium binding constants, exhibit an enthalpy-entropy compensation with a favorable enthalpy at physiological temperatures. The value of -360 cal mol-1 K-1 for delta Cp zero possibly identifies the process as one in which local folding/rearrangement is coupled to complex formation. The 1:1 stoichiometry and thermodynamic parameters provide a basis for understanding the nature of the Fc gamma R-IgG interactions.

Amino Acid Sequence↗

PubMed1995

Catalytic domain of human immunodeficiency virus type 1 integrase: identification of a soluble mutant by systematic replacement of hydrophobic residues.

The integrase protein of human immunodeficiency virus type 1 is necessary for the stable integration of the viral genome into host DNA. Integrase catalyzes the 3' processing of the linear viral DNA and the subsequent DNA strand transfer reaction that inserts the viral DNA ends into host DNA. Although full-length integrase is required for 3' processing and DNA strand transfer activities in vitro, the central core domain of integrase is sufficient to catalyze an apparent reversal of the DNA strand transfer reaction, termed disintegration. This catalytic core domain, as well as the full-length integrase, has been refractory to structural studies by x-ray crystallography or NMR because of its low solubility and propensity to aggregate. In an attempt to improve protein solubility, we used site-directed mutagenesis to replace hydrophobic residues within the core domain with either alanine or lysine. The single substitution of lysine for phenylalanine at position 185 resulted in a core domain that was highly soluble, monodisperse in solution, and retained catalytic activity. This amino acid change has enabled the catalytic domain of integrase to be crystallized and the structure has been solved to 2.5-A resolution [Dyda, F., Hickman, A. B., Jenkins, T. M., Engelman, A., Craigie, R. & Davies, D. R. (1994) Science 266, 1981-1986]. Systematic replacement of hydrophobic residues may be a useful strategy to improve the solubility of other proteins to facilitate structural and biochemical studies.

Amino Acid Sequence↗

PubMed1995

Hydrodynamic studies of a complex between the Fc fragment of human IgE and a soluble fragment of the Fc epsilon RI alpha chain.

The interaction between immunoglobulin E (IgE) and its high-affinity receptor Fc epsilon RI is central to allergic disease. The binding site for Fc epsilon RI lies in the third constant region domain of the epsilon heavy chain of IgE (C epsilon 3). Identical epitopes on the two C epsilon 3 domains in the IgE-Fc are predicted to be on opposite sides of the structure, and therefore each could bind independently to a receptor molecule. Titrations, however, reveal that the IgE-Fc forms an equimolar complex with a soluble fragment of the Fc epsilon RI alpha chain (sFc epsilon RI alpha), and the molecular weight of the complex, as determined by sedimentation equilibrium, confirms this stoichiometry. The measured sedimentation coefficients of the two ligands are in good agreement with computed values for a compact IgE-Fc and an elongated sFc epsilon RI alpha structure. The calculated sedimentation coefficients for possible models of a 1:1 complex lead to exclusion of all highly extended geometries for the complex. Possible explanations for the paradoxical stoichiometry of the IgE-Fc/sFc epsilon RI alpha complex, in terms of the curved shape of IgE, a conformational change in IgE when the receptor binds, and steric interference between two molecules of Fc epsilon RI binding to identical sites, are discussed.

Carbohydrate Sequence↗

PubMed1993

Effect of positive supercoiling on DNA compaction by nucleosome cores.

We have used the analytical ultracentrifuge to measure the ability of histone octamers to compact DNA as a function of DNA supercoiling. Plasmid DNA (3.25 kb) was prepared at various linking numbers (delta Lk), ranging from -35 to +8. Relaxed plasmid (delta Lk = 0) was the least compact. We reconstituted a fixed number of nucleosome cores (either 11 or 13) on these DNAs. The dependence of the frictional coefficient of delta Lk showed that the reconstitute with an initial number of negative supercoils equal to the number of nucleosome cores was the least compact, as expected if each nucleosome core formed requires the constraint of one negative supercoil, resulting in relaxed linker DNA. With DNAs containing an initial number of negative supercoils unequal to the number of nucleosome cores, reconstitutes contained either negative or positive unconstrained supercoils. Reconstitutes with the same number of unconstrained supercoils, whether positive or negative, have similar frictional coefficients and are, therefore, compacted to similar degrees. We conclude that nucleosome cores compact positively and negatively supercoiled DNA equally well. Thus, nucleosome cores formed on positively supercoiled DNA with a superhelical density as high as +0.07 are not significantly unfolded.

Animals↗

PubMed1993

Mode of formation and structural features of DNA-cationic liposome complexes used for transfection.

Complexes formed between cationic liposomes and nucleic acids represent a highly efficient vehicle for delivery of DNA and RNA molecules into a large variety of eukaryotic cells. By using fluorescence, gel electrophoresis, and metal-shadowing electron microscopy techniques, the factors that affect the, yet unclear, interactions between DNA and cationic liposomes as well as the structural features of the resulting complexes have been elucidated. A model is suggested according to which cationic liposomes bind initially to DNA molecules to form clusters of aggregated vesicles along the nucleic acids. At a critical liposome density, two processes occur, namely, DNA-induced membrane fusion, indicated by lipid mixing studies, and liposome-induced DNA collapse, pointed out by the marked cooperativity of the encapsulation processes, by their modulations by DNA-condensing agents, and also by their conspicuous independence upon DNA length. The DNA collapse leads to the formation of condensed structures which can be completely encapsulated within the fused lipid bilayers in a fast, highly cooperative process since their exposed surface is substantially smaller than that of extended DNA molecules. The formation of the transfecting DNA-liposome complexes in which the nucleic acids are fully encapsulated within a positively-charged lipid bilayer is proposed, consequently, to be dominated by mutual effects exerted by the DNA and the cationic liposomes, leading to interrelated lipid fusion and DNA collapse.

Animals↗

PubMed1992

DNA packaging induced by micellar aggregates: a novel in vitro DNA condensation system.

Evidence for a conceptually novel DNA packaging process is presented. X-ray scattering, electron microscopy, and circular dichroism measurements indicate that in the presence of positively charged micellar aggregates and flexible anionic polymers, such as negatively charged polypeptides or single-stranded RNA species, a complex is formed in which DNA molecules are partially embedded within a micellar scaffold and partially condensed into highly packed chiral structures. Based on studies of micelle-DNA and micelle-flexible anionic polymer systems, as well as on the known effects of a high charge density upon the micellar organization, a DNA packaging model is proposed. According to this model, the DNA induces the elongation of the micelles into rodlike aggregates, forming a closely packed matrix in which the DNA molecules are immobilized. In contrast, the flexible anionic polymers stabilize clusters of spherical micelles which are proposed to effect a capping of the rodlike micelles, thus arresting their elongation and creating surfactant-free segments of the DNA that are able to converge and collapse. Thus, unlike other in vitro DNA packaging systems, in which condensation follows encounters between charge-neutralized DNA molecules, a prepackaging phase where the DNA is immobilized within a matrix is proposed in this case. Cellular and nuclear membranes have been implicated in DNA packaging processes in vivo, and negatively charged polyelectrolytes were shown to be involved in the processes. These observations, combined with the basic tenets of the DNA condensation system described here, allow for the progression to the study of more elaborate model systems and thus might lead to insights into the nature and roles of the intricate in vivo DNA-membrane complexes.

Circular Dichroism↗

PubMed1992

Attenuation of DNA-protein interactions associated with intrinsic, sequence-dependent DNA curvature.

Inherently curved DNA segments, associated with short runs of adenines, have been identified in many gene regulatory regions, yet their physiological significance remains unknown. The observations reported in this study indicate that intrinsically bent nucleic acid fragments are characterized by substantially attenuated affinities toward DNA-binding proteins involved in structural functions, such as H1 histone and protamine, as well as toward various DNA-modifying enzymes including ligases and exo- and endonucleases. Two mechanisms might be responsible for the altered binding properties. According to the first mechanism, the attenuated binding affinities and the bending represent two independent consequences of the unique structural parameters exhibited by A-tracts. Indeed, analysis of the degradation products obtained upon exposure of the curved sequences to various chemical nucleases points toward the narrowing of the DNA minor groove, a conformational modulation known to characterize A-tracts and to run along the axially-bent motifs, as a potential determinant of the observed binding attenuation. Alternatively, the conformational constraints which result from the stable bending might act to modulate the strength of DNA-protein interactions. Although the factor directly responsible for the altered binding affinities revealed by the bent sequences cannot as yet be conclusively resolved, it is proposed that a reiteration of this specific factor, being either an A-tract or a bend, in phase with the DNA helical repeat acts to amplify the modulation of the binding.(ABSTRACT TRUNCATED AT 250 WORDS)

Adenine Nucleotides↗

PubMed1992

Nucleic acids packaging processes: effects of adenine tracts and sequence-dependent curvature.

The effects of short runs of adenines (A-tracts) upon nucleic acids packaging processes and the properties of the resulting condensates were investigated by using random DNA sequences isolated from natural sources, as well as synthetic segments obtained by an extensive ligation of specific oligomers. Reiteration of short A-tracts (A(N) where N less than 3) within the DNA molecules is found to be compatible with a long-range chiral organization of the strands in the nucleic acid condensed phases. This chiral order, whose occurrence necessitates a high degree of flexibility, is shown, however, to differ from that exhibited by packed species originating from random AT-rich fragments; the altered patterns are interpreted in terms of a reduced overall flexibility of the DNA strands. Repetition of longer A-tracts (where N greater than 3), in which the distinct structural features that characterize this motif are fully expressed, results in a complete suppression of any chiral order in the packed particles, assigned to a significantly enhanced rigidity. DNA fragments where A-tracts are reiterated in phase, leading to a stable macroscopic curvature, are found to undergo condensation through altered pathways and to form toroidal shapes of unusually small dimensions. The results point towards the intriguing possibility that A-tracts and, in particular, the global, intrinsic curvature associated with such motifs, might be involved in the determination of nucleic acids packaging pathways, and underline the usefulness of defined sequences in the study of DNA condensation processes.

Adenine Nucleotides↗

PubMed1992

Isolation, Purification, and Identification of 2-(p-Hydroxyphenoxy)-5, 7-Dihydroxychromone: A Fungal-Induced Phytoalexin from Cassia obtusifolia.

A single phytoalexin was isolated and purified from 12- to 14-day-old leaves of Cassia obtusifolia L. inoculated with Alternaria cassiae Jurair & Khan. The structure was elucidated by (1)H- and (13)C-nuclear magnetic resonance and mass spectrometry as 2-(p-hydroxyphenoxy)-5,7-dihydroxychromone. The compound was shown to be derived in part from phenylalanine. Radial growth of A. cassiae was inhibited 50% by the compound at 0.3 millimolar. This moderate toxicity is compensated for by the relatively high levels (3 millimolar) accumulated. Phenoxychromones have been previously reported only as constitutive secondary metabolites in Artemisia capillaris Thunb., in which their function is unknown.

Journal Article↗

PubMed1991

Secondary conformational polymorphism of nucleic acids as a possible functional link between cellular parameters and DNA packaging processes.

Circular dichroism and electron microscopy studies of various in vitro DNA packaging systems indicate that all the factors which induce and modulate the secondary conformation of DNA molecules are capable of eliciting nucleic acids condensation processes into tight, highly ordered tertiary structures as well as altering the extent of order and compactness within the resulting species. Specifically, such factors include the ionic strength, the presence of particular dehydrating agents and polyamines, as well as the pH values. It is proposed that slight alterations of these parameters induce the formation of short non-B-DNA segments that propagate as a perturbation along the B-DNA double helix. The structural fluctuations of the dsDNA molecules that result from the conformational discontinuities formed at the junction sites between the B motif and the conformationally altered segments alter the elastic response of the nucleic acids and facilitate cooperative condensation processes. Moreover, the type and frequency of the structurally modified clusters interspersed within the B conformation and determined by the environmental parameters are shown to provide a means for continuous regulation of the extent and mode of DNA packaging. The ionic strength and hydrophobic environment in the close vicinity of the DNA molecules are controlled and modulated in vivo by DNA-binding proteins such as histones and protamines; similarly, pH values and polyamine concentrations are constantly regulated in living systems. It is suggested, therefore, that the secondary structural polymorphism which characterizes the DNA molecules might display a regulatory role by acting as a functional link between cellular parameters and the extent, mode, and timing of nucleic acid packaging processes.

Cadaverine↗

PubMed1990

Extensive interference of DNA packaging processes affected by chemotherapeutic drugs.

The therapeutic and cytotoxic effects exerted by DNA-binding drugs used for chemotherapy originate from a rather large variety of modifications sustained by the nucleic acids upon interaction with the chemical agents. Notably, these modifications are generally considered as involving the following localized chemical or structural processes: base alkylations, frameshift mutations or strand breakages at specific sites, interstrand cross-links, and local structural transitions within the secondary configurations. We find that antitumor agents hinder or prevent altogether the long range packaging of DNA molecules into compact, ordered states. This effect, observed even at low drug to base pair ratios, is general: it is induced by DNA groove binders as well as by intercalators. Nucleoprotein complexes are found to be efficiently protected against the decondensing effect of the drugs. These observations point toward a generic mechanism for the effectiveness of DNA-binding drugs against tumor cells and viruses as well as for the severe effects of chemotherapy on male fertility: actively dividing systems, such as tumor cells, are characterized by regions of chromatin which are decondensed for the purpose of replication and transcription, and therefore accessible to the drugs. Similarly, both viral infection and spermatogenesis, where histones are replaced by protamines, involve transient formation of relatively uncondensed DNA species and subsequent packaging into extremely tight structures.

Chromomycins↗

PubMedDate not supplied

The influence of glycosylation on the thermal stability and effector function expression of human IgG1-Fc: properties of a series of truncated glycoforms.

Antibodies are multifunctional molecules that following the formation of antibody antigen complexes, may activate mechanisms to effect the clearance and destruction of the antigen (pathogen). The IgG molecule is comprised of three globular protein moieties (2Fab+Fc) linked through a flexible hinge region. While the Fabs bind antigens, the Fc triggers effector mechanisms through interactions with specific ligands, e.g. cellular receptors (FcgammaR), and the C1 component of complement. Glycosylation of IgG-Fc has been shown to be essential for efficient activation of FcgammaR and C1. We report the generation of a series of truncated glycoforms of IgG-Fc, and the analysis of the contribution of the residual oligosaccharide to IgG-Fc function and thermal stability. Differential scanning microcalorimetry has been used to compare the stabilities of the homogeneous glycoforms of IgG1-Fc. The results show that all truncated oligosaccharides confer a degree of functional activity, and thermodynamic stability to the IgG1-Fc, in comparison with deglycosylated IgG1-Fc. The same truncated glycoforms of an intact IgG1 anti-MHC Class II antibody are shown to exhibit differential functional activity for FcgammaRI and C1 ligands, relative to deglycosylated IgG1. The minimal glycoform investigated had a trisaccharide attached to each heavy chain and can be expected to influence protein structure primarily in the proximity of the N-terminal region of the C(H)2 domain, implicated as a binding site for multiple effector ligands. These data provide a thermodynamic rationale for the modulation of antibody effector functions by different glycoforms.

Calorimetry, Differential Scanning↗